CILK1 p.Ser174=
c.522T>A · rs766156937 · VCV1680564
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00999%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -5.7, phastCons 0.042 |
| Overall | ||
| CADD | 6.216 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00999%
Admixed American · 6/60,034 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00041%
6/1,461,868 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CILK1
- Protein
- p.Ser174=
- Coding
- c.522T>A
- MANE Select
- NM_014920
- dbSNP
- rs766156937
- Type
- single nucleotide variant
- Location
- chr6:53018471 (GRCh38)
- Gene constraint
- LOEUF 0.774 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.47
- Residue 174
- the protein kinase domain
Similar variants
- CILK1 c.1344-4T>A Uncertain significance ★★ same type
- CILK1 p.Ala629Thr Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg124Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg151Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg262Lys Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg280Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg332Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg475Trp Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cilk1-p-ser174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown